Download Colon Cancer Progression Tutorial

Colon Cancer Progression
Tutorial
The following tutorial walks through a comparison of
gene expression in a primary tumor colon cell line to
that in a metastatic colon cancer cell line. Genes
involved in distinct biological processes, including
cell cycle and telomere maintenance, are
differentially regulated in the progression from
primary tumor growth to metastasis.
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This dataset can be accessed through the
GeneSifter Data Center.
1.
Select Pairwise from the Analysis menu.
2.
Select the magnifying glass icon (
) next
to “U133A” in the list. The data presented
here was generated using the Affymetrix®
GeneChip® Human Genome U133A array.
There are approximately 20,000 transcripts
represented on this array.
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© 2003-2004 VizX Labs, LLC, Seattle, WA. All Rights Reserved
Colon Cancer Tutorial
(continued)
3.
Pairwise analysis is used to identify
differentially expressed genes in two
groups. There are three replicates for each
of the two groups in this study. Select the
three replicates for the primary cell line as
group 1. Select the three replicates for the
metastatic line for group 2.
4.
Pairwise analysis combines a fold-change
cutoff with a quality filter and comparison
statistics to generate a list of differentially
expressed genes. Select the following
settings:
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Normalization: All Median
Normalizes each array to its median
intensity.
Statistics: t-test
Performs a two-sample, unpaired t-test for
each gene that passes the quality and foldchange cutoffs.
Quality: 1
Filters out genes that received absent calls
in both groups.
Threshold: 1.5
Filters out genes with less than a 1.5 fold
change in expression.
Correction: Benjamini and Hochberg
Calculates a false discovery rate from the
raw p-values using the method of
Benjamini and Hochberg.
Data transformation: Log Transform Data
Log base2 transforms the signal values.
5.
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Select the Analyze button
© 2003-2004 VizX Labs, LLC, Seattle, WA. All Rights Reserved
Colon Cancer Tutorial
(continued)
6.
After the analysis is performed a gene list
will be returned. This list contains the genes
that are differentially expressed based on the
pairwise analysis setting selected. 1863
genes passed the filtering criteria – a 1.5 fold
or greater change in expression, present
calls in at least one of the groups and a raw
p-value of at least 0.05 from the t-test. The
genes are sorted by fold change and the first
20 genes in the list are displayed.
7.
To filter the list using the adjusted p value
(false discovery rate), select “adjusted p”
from the pull-down menu and the select the
Search button.
8.
The list filtered on the adjusted p value
contains 1534 genes with a false discovery
rate less than 5%.
9.
To view data and gene summary for any
gene in the list select the Gene Name.
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© 2003-2004 VizX Labs, LLC, Seattle, WA. All Rights Reserved
Colon Cancer Tutorial
(continued)
10.
Selecting a gene from the list will bring up a
data summary and a One-Click Gene
Summary™ for the gene. The One-Click
Gene Summary provides a synopsis of
current UniGene and LocusLink information
for the gene.
11.
Go back to the gene list by clicking the
“Back” button in your browser.
12.
Select the Ontology link to view a
summary of the gene Ontology terms
associated with the genes in the list. See
the online help system for information
about the other reports.
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Note: To view page-specific help
documents for any page, select the
question mark icon ( ) located at the
upper right page corner.
© 2003-2004 VizX Labs, LLC, Seattle, WA. All Rights Reserved
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Colon Cancer Tutorial
(continued
13.
The Ontology Report lists the Gene
Ontology terms associated with the 1534
genes in the pairwise results gene list. See
the help documents for this page for more
information about the Ontology Report.
14.
Click on z-score report.
15.
The z-score report lists the biological
process ontologies that are significantly
over or under-represented in the gene list.
Select the red arrow in the z-score column
to sort the list by z-score for the upregulated genes.
.
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© 2003-2004 VizX Labs, LLC, Seattle, WA. All Rights Reserved
Colon Cancer Tutorial
(continued
16.
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The list is now sorted by z-score for the upregulated genes. The most over or under
represented ontologies are at the top of the
list.
The z-score report shows that there is a
significant enrichment of genes involved
several biological processes, including cell
cycle, RNA processing and telomere
maintenance. The arrow highlights the
“telomerase-dependent telomere
maintenance” ontology which is
significantly over-represented in the upregulated gene list. Select the icon in the
Genes column to view a list of the genes
with this ontology.
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Z-score reports can be generated for the
Molecular Function and Cellular
Component ontologies as well
© 2003-2004 VizX Labs, LLC, Seattle, WA. All Rights Reserved